A list of abbreviations and terms
| 3'-end | The end of a single stranded DNA, where new mononucleotides are attached during enzymatic synthesis of new DNA (  ) |
| 4-MUP | 4-MethylUmbelliferyl Phosphate ( ) |
| 5'-end | The end of a single stranded DNA, where no elongation by enzymatic addition of new mono-nucleotides occurs. This end can be used for labeling or attachment to a solid phase, without altering the usability of the DNA in enzymatic reactions ( ) |
| Agarose gel | A slab of agarose and buffer used to analyze DNA using gel electrophoresis ( ) |
| Amplification (of DNA) | The process of multiplying a specific target sequence ( ) |
| Annealing (in PCR) | Hybridization of primers to the target sequence ( ) |
| AP | Alkaline phosphatase ( ) |
| Asymmetric amplification (of DNA) | DNA Amplification by PCR, where concentrations of the two primers are not equal ( ) |
| Background | The signal detected by the measuring apparatus, which is not generated from the specific reaction, but is always present in the detection ( ) |
| Bands on agarose gel | Double-stranded pieces of DNA of the same length and conformation create uniform bands after electrophoresis in an agarose gel ( ) |
| Biotin | A small chemical substance which can be specifically recognized and bound to Streptavidin ( ) |
| Blank samples | Samples added to an analysis to indicate the level of signal not generated by the specific compound which is analyzed ( ) |
| Blocking (of NucleoLink Strips) | After the covalent binding of the solid phase primer, the Strips are treated with a compound that does not interfere with the later analysis. It will bind to all areas of the NucleoLink surface, which are still able to bind non-specifically ( ) |
| BLV | Bovine Leukemia Virus ( ) |
| BR | Blocking Reagent (Boehringer Mannheim) ( ) |
| BSA | Bovine Serum Albumin ( ) |
| cDNA | Complimentary DNA. DNA synthesized with mRNA as template, to yield the DNA sequence of a transcribed gene ( ) |
| Coating | The act adhering a compound (in DIAPOPS: The solid phase primer) to a surface ( ) |
| Complementary (DNA) | Two pieces of single-stranded DNA's which can recognize and hybridize to each other are complementary |
| Denaturation | The separation of double-stranded DNA into two single strands ( ) |
| Detergent | A compound with both a hydrophilic and a hydrophobic end, able to reduce the surface tension thereby increasing the solubility of hydrophobic substances in water |
| DIAPOPS | Detection of Immobilized Amplified Products in a One Phase System ( ) |
| DNA | DeoxyriboNucleic Acid |
| Double-stranded (DNA) | When two single-stranded DNA molecules have hybridized into double-stranded DNA |
| Descendant | A material (normally Silica-gel) which removes water from the atmosphere, thereby keeping the air dry. Used in small closed containers ( ) |
| EDC | 1-Ethyl-3-(3-Dimethylaminopropyl)-Carbodiimide ( ) |
| ELISA | Enzyme Linked ImmunoSorbent Assay |
| Elongation (in PCR) | The reaction where the primer is extended by addition of mononucleotides in the enzymatic amplification process ( ) |
| False positive results (in PCR and DIAPOPS) | PCR bands on the agarose gel or DIAPOPS results originating from DNA different from the designed target DNA ( ) |
| Fluorescence | Emission of light from a compound in response to illumination with external light |
| Frames (for NucleoLink) | The frames that hold the NucleoLink Strips during handling ( ) |
| Gel electrophoresis | Fragments of DNA are resolved on basis of size or secondary structure by electrophoresis ( ) |
| GeNunc modules | Efficient system for nucleic acid manipulation ( ) |
| Heated lid | A lid on a thermal cycler, which is heated to 100ºC during thermal cycling. This heat is transferred to the top of the PCR vessels, thereby preventing condensation on the inside of the seals of the PCR vessels ( ) |
| HPV | Humane Papilloma Virus ( ) |
| HRP | Horse Radish Peroxidase ( ) |
| Hybridization | The reaction where two single-stranded DNA molecules recognize each other and form a double-stranded DNA ( ) |
| IL2 | Interleukin 2 ( ) |
| Inhibition (of PCR) | The obstruction of the amplification process, normally due to the presence of an agent which blocks the Taq-polymerase ( ) |
| Km | Michaelis constant ( ) |
| Limit of detection (in PCR and DIAPOPS) | The lowest number of target DNA copies necessary to generate a positive signal ( ) |
| Liquid phase PCR products | The products formed in the liquid phase of the DNA amplification. In contrast to the products formed by elongation of the solid phase primer ( ) |
| Lysis | The disrupture of a cell, either prokaryotic or eucaryotic ( ) |
| MeIm | Methyl Imidazole ( ) |
| Melting of DNA | Denaturation ( ) |
| MicroWell | The 96 well format, which fits all equipment for standard ELISA |
| Mononucleotides | The single nucleotides which are the building blocks of DNA |
| MW | Molecular weight ( ) |
| mRNA | Messenger RNA. The processed RNA from a gene transcription which directly codes a protein ( ) |
| NNI | Nalge Nunc International |
| OD | Optical Density |
| Oligonucleotide | A short piece of single stranded DNA, typically 10-40 bases in length ( ) |
| Optimization | The act of improving an analysis or a reaction ( ) |
| PCR* | Polymerase Chain Reaction ( ) |
| PCR mix | The mixture of reagents used in PCR ( ) |
| PCR product | The double stranded DNA of a specific length, which is the product of PCR ( ) |
| PE | Perkin Elmer ( ) |
| Phosphorylation (of the DNA 5'-end) | Addition of a phosphate group to the 5'-end of DNA ( ) |
| Plasmid | A circular double-stranded DNA ( ) |
| Plate reader | An apparatus, which can measure the OD through the single wells in a MicroWell® plate or the fluorescence in each single well. Also called ELISA-reader ( ) |
| pNPP | Para-Nitro Phenyl Phosphate ( ) |
| Pre-Incubation | An incubation with the same buffer, as used in a latter incubation with a reactive compound. The objective is to block all non-specific binding areas on the surface ( ) |
| Primer (in PCR) | A short piece of DNA used to initiate new synthesis of DNA in PCR ( ) |
| Primer-dimer (in PCR) | Short double-stranded DNA formed when annealing between two primers creates a substrate for the PCR enzyme ( ) |
| Probe | Single-stranded DNA designed to hybridize to a target DNA upon analysis of this DNA. The probe is often labeled, in order to be recognized in a later detection step ( ) |
| PVY | Potato Virus Y ( ) |
| Rehybridization (In DIAPOPS) | An additional hybridization detection of the solid phase product formed by PCR amplification of the solid phase primer in DIAPOPS ( ) |
| RNA | RiboNucleic Acid |
| RT | Room temperature |
| Sealing | Closure of a container ( ) |
| Selectivity (in PCR) | How many of the target sequences, in e.g. different bacterial strains, which were intended to be positive in PCR are truly positive ( ) |
| Sensitivity (in PCR) | Least number of copies of the target DNA necessary to generate a positive signal. This is also called the limit of detection ( ) |
| Single-stranded (DNA) | One of the two molecules of the double-stranded DNA |
| Soak-time (in DIAPOPS) | The time in which the NucleoLink Strips are detained containing washing liquid during the washing procedure ( ) |
| Solid phase primer (in DIAPOPS) | The primer which is covalently coupled to the NucleoLink Strips |
| Solid phase product | The PCR products which are covalently bound to the wall of the wells in the NucleoLink Strips after the DNA amplification ( ) |
| Spacer plate | The silicone plate which is placed over the sealed NucleoLink Strips after they have been inserted into the thermal cycler. The spacer plate regulates the pressure on the NucleoLink Strips and sustains the sealing to avoid evaporation ( ) |
| Specificity (in PCR) | The number of false positive reactions generated from target DNA not intended to generate a signal ( ) |
| Stock solution | A solution or buffer of a high concentration of reagents, meant to be stored for longer time and used to prepare the daily used solutions and buffers of a lower concentration |
| Streptavidin | A protein which specifically binds to biotin ( ) |
| Strip (NucleoLink) | A row of 8 wells in one unit ( ) |
| Substrate | The compound or compounds recognized and altered by an enzyme in an enzymatic process ( ) |
| Symmetric DNA amplification (in PCR) | A PCR where the concentrations of the two primers are equal |
| Tape 48 | Heat stable tape for sealing of GeNunc modules ( ) |
| Tape 8 | Heat stable tape for sealing of NucleoLink Strips during thermal cycling in the DNA amplification step of DIAPOPS ( ) |
| Taq-polymerase | A heat stable DNA polymerase from Thermus aquaticus ( ) |
| Target sequence (in PCR) | The DNA sequence that the primers are designed to recognize and amplify ( ) |
| Template DNA (in PCR) | The DNA which is recognized by the PCR primers, and acts as template during the synthesis of a new strand ( ) |
| Thermal cycler | An incubator containing a heat block that fits the vessels in which the PCR is made. The heat incubator must be able to change temperatures rapidly, uniformly and precisely in the PCR vessels during the incubation ( ) |
| TMB | 3,3',5,5'-TetraMethylBenzidine ( ) |
| Tween 20 | A detergent ( ) |
| UNG | Uracil N-Glycosylase ( ) |
| UV-light | Ultra Violet light. Normally light with a wave-length between 100 and 380 nm |
| Vmax | Maximum rate of catalysis of an enzyme ( ) |
| Washing (of NucleoLink Strips) | The act of adding and removing a volume of buffer without any reactive compound ( ) |
*The Polymerase Chain Reaction (PCR) process is covered by US patents owned by Hoffmann-La Roche, Inc and F. Hoffmann-La Roche Ltd.